def exercise_crystallographic():
crystal_symmetry = crystal.symmetry(
unit_cell=(10, 10, 10, 90, 90, 90),
space_group_symbol="P 1 1 2")
sites_frac = flex.vec3_double([
(0.1, 0.1, 0.0),
(0.9, 0.1, 0.0)])
for distance_cutoff in [1,2]:
pair_asu_table = \
crystal_symmetry.special_position_settings().pair_asu_table(
distance_cutoff=distance_cutoff,
sites_frac=sites_frac)
for strictly_in_asu in [True, False]:
cluster = crystal.asu_clusters(
pair_asu_table=pair_asu_table,
strictly_in_asu=strictly_in_asu).sort_index_groups_by_size()
cluster_sizes = [cluster.size() for cluster in cluster.index_groups]
if (distance_cutoff == 1 or strictly_in_asu):
assert cluster_sizes == [1, 1]
else:
assert cluster_sizes == [2]
sites_frac = flex.vec3_double([
(0.1, 0.1, 0.0),
(0.2, 0.2, 0.0),
(0.1, 0.3, 0.0),
(0.9, 0.1, 0.0),
(0.8, 0.2, 0.0)])
for i_trial in xrange(10):
if (i_trial > 0):
sites_frac = sites_frac.select(
flex.random_permutation(size=sites_frac.size()))
for distance_cutoff in [1.5,2]:
asu_mappings = crystal_symmetry.asu_mappings(
buffer_thickness=distance_cutoff).process_sites_frac(
original_sites=sites_frac)
pair_asu_table = crystal.pair_asu_table(
asu_mappings=asu_mappings).add_all_pairs(
distance_cutoff=distance_cutoff)
for strictly_in_asu in [True, False]:
cluster = crystal.asu_clusters(
pair_asu_table=pair_asu_table,
strictly_in_asu=strictly_in_asu).sort_index_groups_by_size()
cluster_sizes = [cluster.size() for cluster in cluster.index_groups]
if (distance_cutoff == 1.5 or strictly_in_asu):
assert cluster_sizes == [3, 2]
else:
assert cluster_sizes == [5]
def exercise_non_crystallographic():
sites_cart = flex.vec3_double([
(7.767, 5.853, 7.671),
(6.935, 5.032, 8.622),
(5.918, 4.176, 8.140),
(7.161, 5.107, 10.012),
(5.126, 3.395, 9.038),
(6.382, 4.336, 10.930),
(5.360, 3.476, 10.439),
(7.956, 7.811, 6.133),
(8.506, 7.237, 5.169),
(8.143, 9.010, 6.428),
(6.253, 5.840, 5.439),
(5.364, 7.253, 5.745),
(5.875, 6.461, 6.183),
(5.216, 5.927, 6.782),
(7.000, 7.000, 7.000)])
have_one_unsorted = False
for i_trial in xrange(10):
if (i_trial > 0):
sites_cart = sites_cart.select(
flex.random_permutation(size=sites_cart.size()))
asu_mappings = crystal.direct_space_asu.non_crystallographic_asu_mappings(
sites_cart=sites_cart)
for distance_cutoff, expected_cluster_sizes in [
(1.0, [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]),
(1.1, [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]),
(1.5, [6, 5, 3, 1]),
(1.6, [15])]:
pair_asu_table = crystal.pair_asu_table(asu_mappings=asu_mappings)
pair_asu_table.add_all_pairs(distance_cutoff=distance_cutoff)
clusters = crystal.asu_clusters(
pair_asu_table=pair_asu_table).sort_index_groups_by_size()
assert [cluster.size() for cluster in clusters.index_groups] \
== expected_cluster_sizes
if (distance_cutoff == 1.5):
for cluster in clusters.index_groups:
sorted_indices = list(cluster)
sorted_indices.sort()
if (list(cluster) != sorted_indices):
have_one_unsorted = True
clusters.sort_indices_in_each_group()
for cluster in clusters.index_groups:
sorted_indices = list(cluster)
sorted_indices.sort()
assert list(cluster) == sorted_indices
assert have_one_unsorted
